Depends on your projects, but if you can preconfigure your chip, it is possible to write your config into the POR and when you turn on your unit, the cypress will have exactly the same config what you set earlier.

Including: input, output config, even states of outputs (as I remember).

So, you need to:

start a setting program, where you configure each cypress chip/ports as inputs/outputs

after you finished the settings, write the config into the POR

et viola, after a power off / on you get the required config back without any manual intervention